Contacts of the strand formed by residues 2293 - 2299 (chain C) in PDB entry 1W21
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL2293 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2093C LEU* 4.7 0.8 - - - +
2288C TYR* 3.9 0.9 - - - +
2289C GLY* 3.2 3.3 - - - -
2290C ALA* 2.8 33.4 + - - +
2291C GLY 3.5 13.0 - - - +
2292C GLY* 1.3 83.4 - - - +
2294C ILE* 1.3 69.4 + - - +
2295C LYS* 4.2 16.6 + - + +
2311C THR* 3.6 29.8 - - + -
2312C ILE 3.9 5.4 - - - +
2313C ASP* 6.0 1.1 - - - -
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Residues in contact with ILE2294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2093C LEU* 3.5 28.3 - - + -
2238C VAL* 3.7 24.2 - - + +
2239C CYS 4.8 0.2 - - - +
2240C HIS* 4.9 1.1 - - + -
2245C PRO* 3.7 32.8 - - + +
2287C CYS* 4.3 8.1 - - + -
2288C TYR 3.4 8.7 - - - +
2292C GLY 4.4 0.2 - - - -
2293C VAL* 1.3 73.9 - - - +
2295C LYS* 1.4 63.1 + - - +
2296C CYS* 4.2 20.9 - - - -
2310C ILE 3.8 0.7 - - - +
2311C THR* 3.5 3.3 - - - -
2312C ILE* 2.7 54.8 + - + +
2314C PRO* 3.8 21.3 - - + +
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Residues in contact with LYS2295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2286C SER 3.7 0.7 - - - +
2287C CYS* 3.2 2.3 - - - -
2288C TYR* 3.0 65.0 + - + +
2293C VAL* 4.2 16.1 + - + +
2294C ILE* 1.4 75.5 - - - +
2296C CYS* 1.3 61.8 + - - +
2297C ILE* 4.1 7.4 - - + -
2309C VAL* 4.8 2.5 - - + -
2310C ILE 3.5 3.6 - - - +
2311C THR* 4.3 17.9 - - + +
2362C LEU* 3.1 26.5 + - + +
2363C ASP* 5.1 1.0 - - - +
2390C GLU* 2.7 39.0 + - - +
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Residues in contact with CYS2296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2247C VAL* 4.1 7.2 - - + -
2285C CYS* 3.8 13.5 - - + -
2286C SER 3.3 4.7 - - - -
2287C CYS* 2.1 44.9 - - - -
2294C ILE* 4.2 4.7 - - - -
2295C LYS* 1.3 74.8 - - - +
2297C ILE* 1.3 63.3 + - - +
2298C CYS* 3.6 5.4 - - - -
2309C VAL* 3.3 5.0 - - - +
2310C ILE* 2.9 40.8 + - + +
2312C ILE* 4.0 25.6 - - - -
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Residues in contact with ILE2297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2284C GLU 4.3 0.2 - - - +
2286C SER 2.9 30.0 + - - +
2288C TYR* 4.3 2.0 - - + -
2295C LYS* 4.1 13.0 - - + +
2296C CYS* 1.3 85.3 - - - +
2298C CYS* 1.3 61.1 + - - +
2307C ARG* 3.7 33.7 - - + -
2308C PRO 3.5 3.6 - - - +
2309C VAL* 4.2 13.9 - - + -
2324C LEU* 4.9 4.9 - - + -
2358C GLY 3.5 8.3 - - - +
2359C PHE* 3.7 19.5 - - - -
2360C ALA* 3.5 39.3 - - + +
2362C LEU* 4.1 16.8 - - + -
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Residues in contact with CYS2298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2282C ILE* 4.1 18.6 - - + -
2283C GLU 3.4 7.0 - - - +
2284C GLU 4.3 2.0 - - - -
2285C CYS* 2.1 50.5 - - - +
2296C CYS* 3.6 14.8 - - - -
2297C ILE* 1.3 76.4 - - - +
2299C ARG* 1.3 63.4 + - - +
2307C ARG* 3.1 34.5 + - - +
2308C PRO* 2.9 19.6 + - + +
2310C ILE* 4.2 8.3 - - - -
2358C GLY 5.3 1.3 - - - -
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Residues in contact with ARG2299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2281C HIS 4.3 1.3 - - - -
2282C ILE 3.6 1.2 - - - -
2283C GLU* 2.9 51.2 + - + +
2284C GLU* 2.7 37.2 + - + +
2298C CYS* 1.3 78.1 - - - +
2300C ASP* 1.3 67.1 - - - +
2301C ASN* 2.8 29.0 + - - +
2307C ARG* 3.7 3.8 - - - +
2308C PRO* 4.2 1.8 - - - -
2331C ASP* 4.4 1.8 - - - +
2354C PRO* 4.8 3.8 - - - +
2355C GLY* 3.3 23.3 + - - +
2356C VAL* 3.6 28.0 - - - +
2357C LYS* 4.6 4.5 - - - -
2412C TYR* 2.9 24.4 + - - -
3477C SIA 3.3 39.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il